I asked Gonetz about the Android port and his response was:
It's too early to talk about it. I just learned to build Mupen64Plus AE from sources.
I foresee problems with port to OGLES since my current work requires OGL 4+
I'm afraid, it will not be straightforward.
So it will probably take quite some time before we see it working on our phones, but he is definitely working on it.